Full QC for 14568_STD_Nidhi-Arianna_Plasma_Pan-cancer_TMT16plex_NS_MP_Eduardo_20230327_18.57

Completed on 2023-03-28 14:32:39


Software

Pipeline DOI: 10.5281/zenodo.3548311 (resolves to latest version)
Software Version
lehtiolab/ddamsproteomics v2.11
Nextflow v22.10.5
MSGF+ v2020.03.14
Dinosaur v1.2.0
Kronik v2.20
Luciphor2 v2020_04_03
Percolator v3.04.0
msstitch v3.11
OpenMS v2.5.0-HEAD-HASH-NOTFOUND-HEAD-HASH-NOTFOUND
DEqMS v1.6.0

Warnings

No warnings

Protein/peptide level QC

Summary

Experiment set Proteins ID and quant. (1%FDR) Proteins ID and quant. (gene centric, 1%FDR) Peptides (unique, 1%FDR) Peptides/protein (unique, median) Peptides/protein (genecentric, unique, median) PSMs (total) PSMs/protein for quant (median) PSMs/protein for quant (genecentric, median)
Set1 5733 5701 32320 3 3 132509 4 3
Set2 1471 1549 13850 3 3 116313 5 4
Set3 1872 1921 16487 3 3 118568 5 4

Overlap

Peptides
IDed in # overlapping sets
1 23208
2 4600
3 10083
Proteins
Proteins ID (1%FDR) IDed in # overlapping sets
4284 1
424 2
1315 3
Gene names
Proteins ID (gene centric, 1%FDR) IDed in # overlapping sets
4296 1
491 2
1299 3
ENSGs
IDed in # overlapping sets
1 4106
2 467
3 1184

PTMs

Summary
PTM site count

Median centered isobaric normalization factors

Peptides
Experiment set Isob. channel Norm. factor
Set1 tmt16plex_126 -0.06086110917296761
Set1 tmt16plex_127N 0.11068622402670059
Set1 tmt16plex_127C -0.02486996838843325
Set1 tmt16plex_128N -0.02300261843959106
Set1 tmt16plex_128C 0.051993806032074374
Set1 tmt16plex_129N -0.09386451090497694
Set1 tmt16plex_129C -0.03983887252272211
Set1 tmt16plex_130N -0.0628405658855451
Set1 tmt16plex_130C 0.049064966096107554
Set1 tmt16plex_131N -0.008130763169126531
Set1 tmt16plex_131C -0.049417308157240214
Set1 tmt16plex_132N -0.15934906282864247
Set1 tmt16plex_132C 0.0
Set1 tmt16plex_133N 0.028840418530721834
Set1 tmt16plex_133C -0.04173666425389655
Set1 tmt16plex_134N -0.21407867451855367
Set2 tmt16plex_126 -0.3211329736357893
Set2 tmt16plex_127N 0.16546092822544844
Set2 tmt16plex_127C -0.3534008217425413
Set2 tmt16plex_128N -0.25184983851384857
Set2 tmt16plex_128C 0.13322427895321098
Set2 tmt16plex_129N -0.18181874162971035
Set2 tmt16plex_129C 0.14169756398416533
Set2 tmt16plex_130N 0.028203888586133985
Set2 tmt16plex_130C -0.7898407451922864
Set2 tmt16plex_131N 0.23637700480522295
Set2 tmt16plex_131C 0.0
Set2 tmt16plex_132N 0.03866017522670617
Set2 tmt16plex_132C -0.13142426882530955
Set2 tmt16plex_133N 0.1522611859231473
Set2 tmt16plex_133C -0.08207070421716622
Set2 tmt16plex_134N 0.23841903282900034
Set3 tmt16plex_126 -0.32089295516491845
Set3 tmt16plex_127N -0.23020358171973232
Set3 tmt16plex_127C -0.002137024372352414
Set3 tmt16plex_128N 0.21908863092821207
Set3 tmt16plex_128C 0.4333034857229898
Set3 tmt16plex_129N -0.11176174268310302
Set3 tmt16plex_129C -0.06601071142346093
Set3 tmt16plex_130N 0.19080910455854472
Set3 tmt16plex_130C 0.24503025661991362
Set3 tmt16plex_131N -0.133240412866229
Set3 tmt16plex_131C 0.3162146478439567
Set3 tmt16plex_132N 0.23088511461111239
Set3 tmt16plex_132C 0.09402128587886249
Set3 tmt16plex_133N 0.15439671969207325
Set3 tmt16plex_133C 0.029918112990890755
Set3 tmt16plex_134N 0.0
Proteins
Experiment set Isob. channel Norm. factor
Set1 tmt16plex_126 -0.0035401536311354675
Set1 tmt16plex_127N 0.09931422285240643
Set1 tmt16plex_127C -0.018227138801556464
Set1 tmt16plex_128N 0.08233497752071628
Set1 tmt16plex_128C 0.0629948023923923
Set1 tmt16plex_129N -0.03937719477776014
Set1 tmt16plex_129C 0.025350091215356585
Set1 tmt16plex_130N 0.03584003712234729
Set1 tmt16plex_130C 0.030014548953740672
Set1 tmt16plex_131N -0.013596490990669619
Set1 tmt16plex_131C -0.06363795297568231
Set1 tmt16plex_132N -0.17226474905452704
Set1 tmt16plex_132C 0.0
Set1 tmt16plex_133N 0.023091892033666017
Set1 tmt16plex_133C -0.050323616757339096
Set1 tmt16plex_134N -0.22441327198422245
Set2 tmt16plex_126 -0.2822219483695818
Set2 tmt16plex_127N 0.15524319881512572
Set2 tmt16plex_127C -0.39831501586605356
Set2 tmt16plex_128N -0.2873310591366418
Set2 tmt16plex_128C 0.09024013031497358
Set2 tmt16plex_129N -0.1827524773101743
Set2 tmt16plex_129C 0.05491846407429879
Set2 tmt16plex_130N 0.05669727488355747
Set2 tmt16plex_130C -0.7912779838872499
Set2 tmt16plex_131N 0.10832798469240146
Set2 tmt16plex_131C 0.0
Set2 tmt16plex_132N 0.0013382673842521342
Set2 tmt16plex_132C -0.13874300866765488
Set2 tmt16plex_133N 0.06352140749877044
Set2 tmt16plex_133C -0.12313516411635561
Set2 tmt16plex_134N 0.11408414397617328
Set3 tmt16plex_126 -0.40546086769885115
Set3 tmt16plex_127N -0.31564241127227
Set3 tmt16plex_127C -0.07125206698409059
Set3 tmt16plex_128N 0.09993592241179527
Set3 tmt16plex_128C 0.4598148699100566
Set3 tmt16plex_129N -0.1659314465336088
Set3 tmt16plex_129C -0.07420644102558605
Set3 tmt16plex_130N 0.17547132784868058
Set3 tmt16plex_130C 0.08906676527034207
Set3 tmt16plex_131N -0.1117417749844618
Set3 tmt16plex_131C 0.1840978210956985
Set3 tmt16plex_132N 0.16662649134470353
Set3 tmt16plex_132C 0.03708678524267839
Set3 tmt16plex_133N 0.1701029426210745
Set3 tmt16plex_133C 0.07009435965353639
Set3 tmt16plex_134N 0.0
Gene names
Experiment set Isob. channel Norm. factor
Set1 tmt16plex_126 -0.002731124041632782
Set1 tmt16plex_127N 0.09919047843961648
Set1 tmt16plex_127C -0.016422312709927667
Set1 tmt16plex_128N 0.08209306806665495
Set1 tmt16plex_128C 0.06305339158036549
Set1 tmt16plex_129N -0.04015423823335418
Set1 tmt16plex_129C 0.02535939789328623
Set1 tmt16plex_130N 0.037095872974676425
Set1 tmt16plex_130C 0.029654637182545684
Set1 tmt16plex_131N -0.012890082725119711
Set1 tmt16plex_131C -0.06287446063258528
Set1 tmt16plex_132N -0.17204749871758285
Set1 tmt16plex_132C 0.0
Set1 tmt16plex_133N 0.02438459775816737
Set1 tmt16plex_133C -0.04926394156034064
Set1 tmt16plex_134N -0.22300724041123487
Set2 tmt16plex_126 -0.28114896387263233
Set2 tmt16plex_127N 0.15771558351159243
Set2 tmt16plex_127C -0.40025909258196357
Set2 tmt16plex_128N -0.28430843825308116
Set2 tmt16plex_128C 0.08612524084707474
Set2 tmt16plex_129N -0.17206613854169817
Set2 tmt16plex_129C 0.05289451797501776
Set2 tmt16plex_130N 0.056884833526407164
Set2 tmt16plex_130C -0.7979119214343751
Set2 tmt16plex_131N 0.1087747074679708
Set2 tmt16plex_131C 0.0
Set2 tmt16plex_132N -0.0021823519653842993
Set2 tmt16plex_132C -0.14179872892638912
Set2 tmt16plex_133N 0.06774053907820132
Set2 tmt16plex_133C -0.11807356428317561
Set2 tmt16plex_134N 0.11209522257849969
Set3 tmt16plex_126 -0.40135222107239965
Set3 tmt16plex_127N -0.31303040853791764
Set3 tmt16plex_127C -0.06435691886114014
Set3 tmt16plex_128N 0.1093655402450775
Set3 tmt16plex_128C 0.46303219056908773
Set3 tmt16plex_129N -0.1667732021920214
Set3 tmt16plex_129C -0.0737773196727094
Set3 tmt16plex_130N 0.176668274783216
Set3 tmt16plex_130C 0.08930865392695075
Set3 tmt16plex_131N -0.1050000771453341
Set3 tmt16plex_131C 0.1846565934831368
Set3 tmt16plex_132N 0.16724100593116464
Set3 tmt16plex_132C 0.04257811633491748
Set3 tmt16plex_133N 0.17663638697015926
Set3 tmt16plex_133C 0.0772691409264814
Set3 tmt16plex_134N 0.0
ENSGs
Experiment set Isob. channel Norm. factor
Set1 tmt16plex_126 -0.004400699449474299
Set1 tmt16plex_127N 0.09932979768127126
Set1 tmt16plex_127C -0.015633906493410787
Set1 tmt16plex_128N 0.08115514617969577
Set1 tmt16plex_128C 0.06504867933239611
Set1 tmt16plex_129N -0.04148981775079985
Set1 tmt16plex_129C 0.023125895349230152
Set1 tmt16plex_130N 0.03549973080571611
Set1 tmt16plex_130C 0.030394955409101865
Set1 tmt16plex_131N -0.011730512923685765
Set1 tmt16plex_131C -0.06384573204702004
Set1 tmt16plex_132N -0.17221176921115777
Set1 tmt16plex_132C 0.0
Set1 tmt16plex_133N 0.023434838180903306
Set1 tmt16plex_133C -0.04916089331046791
Set1 tmt16plex_134N -0.2230735457082602
Set2 tmt16plex_126 -0.29397624167102343
Set2 tmt16plex_127N 0.15231059694076254
Set2 tmt16plex_127C -0.4094412751364622
Set2 tmt16plex_128N -0.2843889019706545
Set2 tmt16plex_128C 0.07724258674553575
Set2 tmt16plex_129N -0.16362039211850465
Set2 tmt16plex_129C 0.04631986754546347
Set2 tmt16plex_130N 0.05409065551472203
Set2 tmt16plex_130C -0.8129045085526041
Set2 tmt16plex_131N 0.11543863095661244
Set2 tmt16plex_131C 0.0
Set2 tmt16plex_132N -0.014493024122090858
Set2 tmt16plex_132C -0.16182067264067346
Set2 tmt16plex_133N 0.07014273705065044
Set2 tmt16plex_133C -0.12481953902296894
Set2 tmt16plex_134N 0.10387834581068667
Set3 tmt16plex_126 -0.3941063584955984
Set3 tmt16plex_127N -0.3081277164344538
Set3 tmt16plex_127C -0.054331702815025196
Set3 tmt16plex_128N 0.12288565037373189
Set3 tmt16plex_128C 0.4632743673687898
Set3 tmt16plex_129N -0.16986047687796102
Set3 tmt16plex_129C -0.07162532036410241
Set3 tmt16plex_130N 0.18004583994448264
Set3 tmt16plex_130C 0.09858150453208747
Set3 tmt16plex_131N -0.1050000771453341
Set3 tmt16plex_131C 0.19960285549365953
Set3 tmt16plex_132N 0.1643994359582095
Set3 tmt16plex_132C 0.056508653197749226
Set3 tmt16plex_133N 0.18295462898346315
Set3 tmt16plex_133C 0.09553249551893472
Set3 tmt16plex_134N 0.0

Identifications

Peptides
Proteins
Gene names
ENSGs

Precursor area intensity

Peptides
Proteins
Gene names
ENSGs

Isobaric intensities

Peptides
Proteins
Gene names
ENSGs

Isobaric normalization factors

Peptides
Proteins
Gene names
ENSGs

# PSMs used for isobaric quantitation per identification

Peptides
Proteins
Gene names
ENSGs

# PSMs used for isobaric quantitation per identification for only complete overlapping set

Peptides
Proteins
Gene names
ENSGs

Percentage of identifications with >1 quantifying PSM in the complete overlapping set

Peptides
Proteins
Gene names
ENSGs

# peptides with MS1 quant per protein (top 3 used)

Peptides
Proteins
Gene names
ENSGs

Principal component analysis

Peptides
Proteins
Gene names
ENSGs

Overall protein coverage


PSM level QC

# PSMs and scans
Isobaric missing values
Missed cleavages

Retention time

Plate: Set1_3-10
Plate: Set2_3-10
Plate: Set3_3-10

Precursor error

Plate: Set1_3-10
Plate: Set2_3-10
Plate: Set3_3-10

LC full width at half max (FWHM)

Plate: Set1_3-10
Plate: Set2_3-10
Plate: Set3_3-10

Fraction yield

Plate: Set1_3-10
Plate: Set2_3-10
Plate: Set3_3-10

MSGF Score

Plate: Set1_3-10
Plate: Set2_3-10
Plate: Set3_3-10

Precursor ion fraction

Plate: Set1_3-10
Plate: Set2_3-10
Plate: Set3_3-10